10-48731094-T-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001394531.1(WDFY4):c.1130-16T>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 1,506,186 control chromosomes in the GnomAD database, including 158,839 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001394531.1 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WDFY4 | NM_001394531.1 | c.1130-16T>A | splice_polypyrimidine_tract_variant, intron_variant | ENST00000325239.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WDFY4 | ENST00000325239.12 | c.1130-16T>A | splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001394531.1 | P1 | |||
WDFY4 | ENST00000360890.6 | c.1130-16T>A | splice_polypyrimidine_tract_variant, intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.475 AC: 72251AN: 152028Hom.: 17640 Cov.: 33
GnomAD3 exomes AF: 0.440 AC: 56549AN: 128612Hom.: 12835 AF XY: 0.445 AC XY: 29813AN XY: 66940
GnomAD4 exome AF: 0.454 AC: 615359AN: 1354042Hom.: 141194 Cov.: 32 AF XY: 0.456 AC XY: 301736AN XY: 661734
GnomAD4 genome ? AF: 0.475 AC: 72291AN: 152144Hom.: 17645 Cov.: 33 AF XY: 0.475 AC XY: 35320AN XY: 74372
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at